They violate fundamental principles of user interface design.

Principle 1: Leave the user in control. It's your screen. You decide what's on it. They're your windows. You set their sizes and stacking order. It's your mouse. You put it where you want it.

Principle 2: One action should give one result. When you click on something and two windows open, you're getting more than you asked for... or wanted. When a timer hidden in a web page loads something new -- something you didn't ask for -- your action (viewing the page) got more results than you expected.

There sure are lots of annoying things web sites do that violate these fundamentals.